ModelCHECK Gatekeeper is working most of the time, but..........

We recently turned on ModelCheck Gatekeeper in Windchill.  Got all the settings correctly entered in .mch , .mcs and config_init.mc .  For most part it is working fine, but we are running into some sporadic files that will not check-in from Creo3.  Even if the parameter MC_Verified is set to yes, it will not check-in.  We have to modify the file again, then either run modelcheck interactive, regen, save and then will check-in.  

Also alot of family tables are problematic, save and verifying the table will change the MC_Verified to yes, but will not check-in, have to bring up each instance, modify, then either run modelcheck interactive, regen, save and then will family table will check-in.

Is anyone experiencing this, any solution?